AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i296_tpal_bbur_300.orf -o296_tpal_bbur_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTP00382 170 AE000520 #2 RTP00949 206 AE000520 Motif number 1 GGAGCGCGAGCGCAGCCACGTCGAGCACATTA 1 34 0 CGCGCACGTC 0.997138 -137 TTTAAGATCACGGTGGTGGAGCGCGAGCGCAG 1 51 0 CGGGTGGAGC 0.982924 -120 AAGAAGAACACCGGGACACGGCGGAGAAAACG 1 89 0 CCGGCACGGC 0.990965 -82 ATTTTGAAAACGGATACACGTCAAATTACCTG 1 125 0 CGGTCACGTC 0.969142 -46 GCTTTCAGGCGCTGGCGGATGCGTATTTTGA 1 150 0 CGCGCGGATG 0.988461 -21 TGGGCGTCGACGCCGACACGTCTTGATTCACT 2 69 0 CGCGCACGTC 0.997133 -138 CTGTTCCGGCCGGAGCTGGGGCTAGAGTTTGC 2 123 0 CGGGTGGGGC 0.991235 -84 ACAGCAAACTCCCTGCCGCAGGCTTTTTAATC 2 151 1 CCCGCGCAGG 0.976529 -56 AATTATTTGGCGCAAGCGGATCATACTGAG 2 187 1 CGCACGGATC 0.969142 -20 *** * ****** Masking position 1 Map Score: 14.7309 Number of sites scoring better than the average of aligned sites = 1133 Number in coding regions = 359 Number in noncoding regions = 774 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 2 AGCGCGAGCGCAGCCACGTCGAGCACATTA 1 34 0 CAGCCACGTC 0.987402 -137 CTGCGCTCGCGCTCCACCACCGTGATCTTA 1 51 1 GCTCCACCAC 0.983661 -120 GAAGAACACCGGGACACGGCGGAGAAAACG 1 89 0 GGGACACGGC 0.979587 -82 TTTGAAAACGGATACACGTCAAATTACCTG 1 125 0 GATACACGTC 0.925606 -46 AAATACGCATCCGCCAGCGCCTGAAAGC 1 153 1 CCGCCAGCGC 0.987221 -18 AATACGCAAAACTCCACGACACCCGCATTG 2 22 1 ACTCCACGAC 0.934609 -185 GGCGTCGACGCCGACACGTCTTGATTCACT 2 69 0 CCGACACGTC 0.989495 -138 TCGGCGTCGACGCCCACCGCAACGAAAAAA 2 85 1 CGCCCACCGC 0.984074 -122 GCAAACTCTAGCCCCAGCTCCGGCCGGAAC 2 123 1 GCCCCAGCTC 0.955061 -84 ********** Masking position 6 Map Score: 13.0155 Number of sites scoring better than the average of aligned sites = 2148 Number in coding regions = 617 Number in noncoding regions = 1531 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 3 TGTATTCTTCGTTCCCTTAATG 1 2 1 GTATTCTCGT 0.980148 -169 AAACGAAAGCGTTTTCTCCGCCGTGTCCCGG 1 80 1 GTTTTCTCGC 0.995246 -91 CCGTGTCCCGGTGTTCTTCTTTGTTCAGGTA 1 100 1 GTGTTCTCTT 0.933433 -71 TGGGGCTAGAGTTTGCAACGCCCTTTTTTTC 2 108 0 GTTTGCACGC 0.987817 -99 GCGGCAGGGAGTTTGCTGTTCCGGCCGGAGC 2 139 0 GTTTGCTTTC 0.945085 -68 CTCAGTATGATCCGCTTGCGCCAAA 2 192 0 GTATGATCGC 0.972636 -15 ******* *** Masking position 4 Map Score: 4.36624 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 72 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 TTATCATTAAGGGAACGAAGAATACA 1 6 0 GGGAACAAGA 0.991678 -165 CTCCACCACCGTGATCTTAAACGAAAGCGTT 1 62 1 GTGATCTAAA 0.816644 -109 GTCAAATTACCTGAACAAAGAAGAACACCGG 1 107 0 CTGAACAAGA 0.977741 -64 CCACGACACCCGCATTGAAGTATCAGAGACA 2 35 1 CGCATTAAGT 0.747168 -172 GAGACAAACAGTGAATCAAGACGTGTCGGCG 2 60 1 GTGAATAAGA 0.96544 -147 CGACGCCCACCGCAACGAAAAAAAGGGCGTT 2 92 1 CGCAACAAAA 0.94881 -115 AAATAATTTGGGGATTAAAAAGCCTGCGGCA 2 164 0 GGGATTAAAA 0.955463 -43 ****** **** Masking position 4 Map Score: 2.17003 Number of sites scoring better than the average of aligned sites = 811 Number in coding regions = 234 Number in noncoding regions = 577 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 CGTGGCTGCGCTCGCGCTCCACCACCGTGA 1 46 1 CTCGCGCTCC 0.993457 -125 CCTTGAGCCTCAATACGCAAA 2 2 1 CTTGAGCCTC 0.989659 -205 GCGTTGCAAACTCTAGCCCCAGCTCCGGCC 2 118 1 CTCTAGCCCC 0.990265 -89 GTATGATCCGCTTGCGCCAAATAATTTGGG 2 183 0 CTTGCGCCAA 0.970792 -24 ********** Masking position 2 Map Score: 1.59942 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 30 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 ********** No masking Map Score: 8.26662e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 ********** No masking Map Score: 8.26662e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ********** No masking Map Score: 8.26662e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0